In silico simulation of

Subtracted Restriction Fingerprinting (SRF)

Subtracted Restriction Fingerprinting (SRF) is a typing technique recently described by Terletski et al. (2003). Check their article for more info.

SRF is a genotyping technique based on double endonuclease digestion of genome. The endonucleases used in this simulation program are all palinfromic, and they show no degenerated nucleotides. We will describe briefly this technique:
  • DNA is double digested with endonucleases.
  • One endonuclease cleaves genome very frequently and the other one fewer times.
  • One restriction enzyme (RE1) allows performing a filling reaction with digoxigenin labelled Uridine (Dig-dUTP) and the other restriction enzyme allows a filling reaction with biotinilated Cytosine (Bio-dCTP).
  • From the four types of fragments yielded after digestion, RE1-RE2, RE2-RE1 and RE2-RE2 fragments (labelled in one or both ends with biotin) are captured by streptavidin-coated magnetic beads (they are substracted).
  • Remaining RE1-RE1fragments (with are labelled in both end with digoxigenin) will be separated by electrophoresis, transfered by shouthern blot, stained  and  bands pattern analysed.
SRF suggestion tool

The SRF suggestion tool  will provide researches with a list of endonuclease pairs suitable for SRF fingerprinting of selected genome. Following the links, theoretical electrophoretic pattern and identity of bands (sequence and ORF) may be optained.

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